Search

High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies. [ABSTRACT FROM AUTHOR]

The pantropical plant genus Dalbergia comprises approximately 250 species, most of which have a high economic and ecological value. However, these species are among the most threatened due to illegal logging and the timber trade. To enforce protective legislation and ensure effective conservation of Dalbergia species, the identity of wood being traded must be accurately validated. For the rapid and accurate identification of Dalbergia species and assessment of phylogenetic relationships, it would be highly desirable to develop more effective DNA barcodes for these species. In this study, we sequenced and compared the chloroplast genomes of nine species of Dalbergia. We found that these chloroplast genomes were conserved with respect to genome size, structure, and gene content and showed low sequence divergence. We identified eight mutation hotspots, namely, six intergenic spacer regions (trnL-trnT, atpA-trnG, rps16-accD, petG-psaJ, ndhF-trnL, and ndhG-ndhI) and two coding regions (ycf1a and ycf1b), as candidate DNA barcodes for Dalbergia. Phylogenetic analyses based on whole chloroplast genome data provided the best resolution of Dalbergia, and phylogenetic analysis of the Fabaceae showed that Dalbergia was sister to Arachis. Based on comparison of chloroplast genomes, we identified a set of highly variable markers that can be developed as specific DNA barcodes. [ABSTRACT FROM AUTHOR]

Three pairs of generic primers designed for specific reverse transcription polymerase chain reaction amplification of part of the cytorhabdoviruses genomes were successfully tested with a number of red clover samples. Two infected plants showing irregular vein clearing, tissue necrosis and stunted growth symptoms were selected for further studies. Subsequently, two novel plant rhabdoviruses, tentatively named Trifolium pratense virus A (TpVA) and Trifolium pratense virus B (TpVB), were detected in red clover plants. Sequence analyses of nucleotide sequences of their genomic RNAs obtained after high‐throughput sequencing confirmed their affinity to members of the genus Cytorhabdovirus. While TpVA was transmitted by mechanical inoculation to Nicotiana occidentalis 37B and subtransferred to Physalis floridana plants, crude sap transmission of TpVB to a range of herbaceous host plants failed. The bacilliform shape of virions, which has a cytoplasm‐limited distribution, their sizes, and the phylogenetic relationships, support assignment of TpVA and TpVB to two distinct species of the genus Cytorhabdovirus. [ABSTRACT FROM AUTHOR]

In many lichen-forming fungi, molecular phylogenetic analyses lead to the discovery of cryptic species within traditional morphospecies. However, in some cases, molecular sequence data also questions the separation of phenotypically characterised species. Here we apply an integrative taxonomy approach - including morphological, chemical, molecular, and distributional characters - to re-assess species boundaries in a traditionally speciose group of hair lichens, Bryoria sect. Implexae. We sampled multilocus sequence and microsatellite data from 142 specimens from a broad intercontinental distribution. Molecular data included DNA sequences of the standard fungal markers ITS, IGS, GAPDH, two newly tested loci (FRBi15 and FRBi16), and SSR frequencies from 18 microsatellite markers. Datasets were analysed with Bayesian and maximum likelihood phylogenetic reconstruction, phenogram reconstruction, STRUCTURE Bayesian clustering, principal coordinate analysis, haplotype network, and several different species delimitation analyses (ABGD, PTP, GMYC, and DISSECT). Additionally, past population demography and divergence times are estimated. The different approaches to species recognition do not support the monophyly of the 11 currently accepted morphospecies, and rather suggest the reduction of these to four phylogenetic species. Moreover, three of these are relatively recent in origin and cryptic, including phenotypically and chemically variable specimens. Issues regarding the integration of an evolutionary perspective into taxonomic conclusions in species complexes, which have undergone recent diversification, are discussed. The four accepted species, all epitypified by sequenced material, are Bryoria fuscescens, B. glabra, B. kockiana, and B. pseudofuscescens. Ten species rank names are reduced to synonymy. In the absence of molecular data, they can be recorded as the B. fuscescens complex. Intraspecific phenotype plasticity and factors affecting the speciation of different morphospecies in this group of Bryoria are outlined. [ABSTRACT FROM AUTHOR]

• Mitochondrial monophyly is commonly employed to define evolutionary significant units. • Monophyly may be caused by insufficient sampling or a recent common ancestor. • Mitogenomic studies are generally based on few samples and prone to sampling issues. • Expanded mitogenome sampling negates previous monophyly in fin whales. The advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in such mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point was illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013), which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 380 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para- or polyphyly) can lead to erroneous conclusions due to relatively "trivial" aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to the most recent common ancestor and hence the probability that individuals in a sample are monophyletic. [ABSTRACT FROM AUTHOR]

• Cyto-nuclear conflicts occurred in Stewartia s. l. phylogeny. • Hartia was nested in Stewartia s.s. with the basal S. malacodendron in America. • Introgression was prevailing in shallow phylogeny with a consistent backbone. • Ancient co-distribution and dispersal contributed to introgression in Asian. Phylogenetic analyses using diverse datasets can yield conflicting inference of evolutionary history. Phylogenetic conflicts observed in both animal and plant systems have often been explained by two competing (but not mutually exclusive) hypotheses, i.e., hybridization vs. incomplete lineage sorting (ILS). The likelihood of either process contributing to phylogenetic conflict in a given group is context-dependent, involving attributes of life history, distribution, and phylogeny, among others. Here we explore phylogenetic conflict in Stewartia s.l. , a genus with ca. 20 species of trees and shrubs from the tea family (Theaceae) disjunctly distributed between eastern Asia (EAS) and eastern North America (ENA). We use both restriction-site associated DNA sequencing (RAD-seq) and complete plastome sequence data to reconstruct the phylogeny of the group using concatenation and coalescence approaches. Our results indicate strong conflicts between the topologies reconstructed using nuclear and plastid data. Four-taxon D -statistic (ABBA-BABA) tests detected prevailing signals of introgression. Bayesian Analysis of Macro-evolutionary Mixtures (BAMM) inferred that species diversification occurred in the middle to late Miocene. Ancestral range reconstructions indicated co-distribution of ancestral species (represented by internal nodes) for both the Hartia clade (in southern China) and the EAS Stewartia s.s. clade (Japan Archipelago and the Yangtze Valley of China). The latter clade experienced multiple events of dispersal and vicariance during its diversification history. Ancient introgressive hybridization following species diversification in the mid- to late-Miocene likely caused diverging histories in the nuclear and plastid genomes, leading to phylogenetic conflict in Stewartia s.l. Our study indicates that species diversification driven by both the intensification of the East Asian summer monsoon since the late Miocene and reduced risks of extinction due to frequent dispersal possibly via East China Sea Land Bridge impacted the anomalous species richness between EAS and ENA. Our study highlights the importance of using data from different genomes while reconstructing deep and shallow phylogenies of organisms. [ABSTRACT FROM AUTHOR]

Pristimantis is the most diverse genus of tetrapods comprising 532 described species. It contains a large number of morphologically cryptic species that are being discovered with the assistance of genetic evidence. We use molecular, morphological, bioacoustic, and environmental data to assess the phylogenetic relationships and determine the species within an Andean clade of Pristimantis, which is distributed from central Ecuador to northern Peru. We assign to this clade the name Huicundomantis and propose it as a subgenus. Our results show that Huicundomantis is composed of two large clades which we name as the P. phoxocephalus species group and the P. cryptomelas species group. Huicundomantis is composed of 28 species of which 12 have been described and 16 are new. We describe 11 of these undescribed species. The most effective characters to discriminate among species are DNA sequences, qualitative morphology, and advertisement calls. Morphometric and environmental characters are not very useful to define species limits. We clarify the identity of P. riveti and show that populations from southern Ecuador traditionally ascribed to P. riveti are a new species, P. lutzae sp. nov. We also show that P. prometeii is a junior synonym of P. hampatusami. The current diversity and geographic distribution of Huicundomantis are consistent with a model of allopatric speciation. All species have a restricted distribution range (less than 4330 km2) and are assigned to the Red List categories Data Deficient or threatened with extinction. We provide new reasons to increase conservation efforts for these species and their habitat. Taking our results into account, Pristimantis species richness in Ecuador increases from 211 to 221 species, and the number of species endemic to Ecuador from 119 to 129. [ABSTRACT FROM AUTHOR]

We obtained and analyzed whole genome data for more than 160 representatives of skipper butterflies (family Hesperiidae) from all known subfamilies, tribes and most distinctive genera. We found that two genera, Katreus Watson, 1893 and Ortholexis Karsch, 1895, which are sisters, are well-separated from all other major phylogenetic lineages and originate near the base of the Hesperiidae tree, prior to the origin of some subfamilies. Due to this ancient origin compared to other subfamilies, this group is described as Katreinae Grishin, subfam. n. DNA sequencing of primary type specimens reveals that Ortholexis melichroptera Karsch, 1895 is not a female of Ortholexis holocausta Mabille, 1891, but instead a female of Ortholexis dimidia Holland, 1896. This finding establishes O. dimidia as a junior subjective synonym of O. melichroptera. Furthermore, we see that Chamunda Evans, 1949 does not originate within Pyrginae Burmeister, 1878, but, unexpectedly, forms an ancient lineage of its own at the subfamily rank: Chamundinae Grishin, subfam. n. Finally, a group of two sister genera, Barca de Nicéville, 1902 and Apostictopterus Leech, [1893], originates around the time Hesperiinae Latreille, 1809 have split from their sister clade. A new subfamily Barcinae Grishin, subfam. n. sets them apart from all other Hesperiidae. [ABSTRACT FROM AUTHOR]

Abstract Angiostrongylus cantonensis is the main causative agent of human angiostrongyliasis. A sibling species, A. malaysiensis has not been unequivocally incriminated to be involved in human infections. To date, there is only a single report on the application of the partial 66-kDa protein gene sequence for molecular differentiation and phylogeny of Angiostrongylus species. Nucleotide sequences of the 66-kDa protein gene of A. cantonensis and A. malaysiensis from Thailand, as well as those of the laboratory strains of A. cantonensis from Thailand and Hawaii, A. cantonensis from Japan and China, A. malaysiensis from Malaysia, and A. costaricensis from Costa Rica, were used for the reconstruction of phylogenetic tree by the maximum likelihood (ML) method and the haplotypes by the median joining (MJ) network. The ML phylogenetic tree contained two major clades with a full support bootstrap value – (1) A. cantonensis and A. malaysiensis , and (2) A. costaricensis. A. costaricensis was basal to A. cantonensis and A. malaysiensis. The genetic distance between A. cantonensis and A. malaysiensis ranged from p =.82% to p = 3.27%, that between A. cantonensis and A. costaricensis from p = 4.90% to p = 5.31%, and that between A. malaysiensis and A. costaricensis was p = 4.49% to p = 5.71%. Both A. cantonensis and A. malaysiensis possess high 66-kDa haplotype diversity. There was no clear separation of the conspecific taxa of A. cantonensis and A. malaysiensis from different geographical regions. A more intensive and extensive sampling with larger sample size may reveal greater haplotype diversity and a better resolved phylogeographical structure of A. cantonensis and A. malaysiensis. Graphical abstract Unlabelled Image Highlights • Angiostrongylus cantonensis is the main causative agent of human angiostrongyliasis • Angiostrongylus malaysiensis has not been unequivocally incriminated to be involved in human infections • 66-kDa gene reveals Angiostrongylus costaricensis to be basal to A. cantonensis and A. malaysiensis • There was no clear separation of the conspecific taxa from different geographical regions • Both Angiostrongylus cantonensis and A. malaysiensis possess high 66-kDa haplotype diversity [ABSTRACT FROM AUTHOR]

Abstract The internal transcribed spacers are highly preferred nuclear markers for the phylogenetic assessment of most eukaryotes, including plants. More recently, ITS2 has shown to possess equivalent phylogenetic significance as the entire ITS region. Vigna mungo L. Hepper is comparatively less explored from the molecular aspects as compared to the other species of the Vigna genus. The study presents the intra-individual characterization of 24 distinct genotypes Vigna mungo L. Hepper, using morphological as well as nrDNA ITS2 sequences and secondary structural data. The morphological characterization has been carried out using nine important agro-morphological traits. The molecular phylogeny of the sequence data, using the maximum parsimony and neighbor joining methods, shows the significant distinction based on the haplotypic variations amongst blackgram genotypes. The ITS2 secondary structures predicted using the homology modeling approach were compatible with the eukaryote-universal ITS2 secondary structure. The sequence-structure phylogeny reconstructed using the profile neighbour joining approach, also showed the presence of haplotypic variations in form of clusters on the phylogenetic tree. Further, the high GC content in the sequence data and highly negative ΔG values of the folded secondary structures ruled out the possibilities of the presence of any pseudogenes in the data set. Our analysis recommends the use of ITS2 sequence and secondary structure data at the intraspecific levels of plant taxonomical classification. Moreover, this study for the very first time reports the combined use morphological, and molecular data (using ITS2 sequence and secondary structural information) for the characterization of plants at the varietal level of taxonomical classification. [ABSTRACT FROM AUTHOR]

The nuclear ribosomal DNA (nrDNA) internal transcribed spacers (ITS) sequences is extensively used in the plant molecular phylogenetics for plant taxonomic identification and DNA barcoding purposes because the nrDNA ITS gene is easy to amplify by using the universal primers, its length is shorter and thus easy to sequence, and has strong discrimination power to distinguish the taxon at the species level. The present molecular phylogenetic analysis of ITS nrDNA sequences focuses to determine the taxonomic status of an unresolved endemic taxon Kickxia abhaica D.A. Sutton (Family Plantaginaceae, tribe Antirrhineae) reported from Saudi Arabia. The analysis supports the transfer of K. abhaica under the genus Nanorrhinum. [ABSTRACT FROM AUTHOR]

The molecular phylogeny of Bacidia s.s. in the Russian Far East was investigated using 62 nucleotide sequences from the ITS nrDNA region, 22 of which were newly obtained. Phylogenetic reconstructions employed Bayesian inference and maximum likelihood searches using MrBayes and RAxML. In addition, ITS2 secondary structures added further support using Compensatory Base Changes. As a result of morphological and phylogenetic studies, four new species of Bacidia are described. Bacidia areolata sp. nov. belongs to the suffusa group. It was collected once in Khabarovskiy Krai, the Russian Far East, on the bark of Acer tegmentosum and is closely related to B. suffusa but differs in having a smooth, cracked to areolate thallus and shorter spores. Bacidia elongata sp. nov. is a member of the fraxinea group and is similar to B. fraxinea but differs in having a wide zone of cells with enlarged lumina along the edge of the exciple. In fact, this zone of enlarged cells, in combination with its overall habit, places it morphologically close to B. suffusa , B. millegrana and B. campalea. Bacidia kurilensis sp. nov. is a basal member of the laurocerasi group and closely related to B. biatorina , B. heterochroa , B. laurocerasi and B. salazarensis. However, the combination of a granular thallus, large black apothecia and a green hue in the upper part of the exciple edge as well as in the epihymenium sets it apart from the species mentioned above. Bacidia sachalinensis sp. nov. resolves as a strongly supported member of the polychroa group and is known from a single locality in Sakhalin, the Russian Far East. Its thallus structure and apothecium colour are variable, which is typical for the polychroa group, but it differs from B. polychroa by having shorter spores with fewer septa and a mainly smooth to areolate thallus. [ABSTRACT FROM AUTHOR]

Challenges in morphology come to bear when assigning specific names in foliose Bangiales. Recent studies suggest that the integration of molecular and phenotypic data is essential, particularly in setting species boundaries and revealing the true species diversity of a given area. In an attempt to further elucidate the diversity of foliose Bangiales in the Philippines, two new species, Pyropia lunae sp. nov. and Pyropia islae sp. nov. are described. Each species differs from other closely related taxa by a combination of morphological and anatomical characters, and nucleotide sequences. Phylogenetic reconstruction based on rbcL gene sequences supports the sister relationship of P. lunae and Pyropia acanthophora, whereas P. islae is recovered as a species allied to Pyropia tanegashimensis and Pyropia denticulata. These two previously undescribed species increase the number of confirmed Philippine Pyropia species to four. So far, P. lunae and P. islae are found only from the Batanes Islands while P. acanthophora and P. tanegashimensis are known to extend their native distributions across into the Indo-Pacific waters. Questions remain, however, with regard to the true species diversity of foliose Bangiales in the Philippines. A wider sampling effort and the application of molecular methods will make it possible to resolve the remaining gaps in the taxonomy of Philippine foliose Bangiales. [ABSTRACT FROM AUTHOR]

The genera Coppinsiella and Seawardiella are described based on the combined phylogenetic analysis from ITS nrDNA, 28S nrLSU and 12S mtSSU sequences. The affinities of the new genera Orientophila, Athallia, Flavoplaca and Calogaya are discussed. The former Caloplaca lobulata group (or 'Xanthoria lobulata-Gruppe' sensu Steiner et Poelt 1982) found to be positioned in the Calogaya clade based on ITS phylogeny while after a three gene phylogeny (based on ITS nrDNA, nrLSU and mtSSU sequences) two species (i.e.: Seawardiella lobulata and described as new S. tasmaniensis) were located in the Seawardiella clade of the Xanthorioideae. Three other species (i.e. Lazarenkoella zoroasteriorum, L. persica and L. polycarpoides) were positioned in the Lazarenkoella-clade of the Brownlielloideae. The position of all species of the Calogaya clade (after ITS phylogeny) should be re-evaluated based on three gene phylogeny from ITS nrDNA, nrLSU and mtSSU sequences. The new species Seawardiella tasmaniensis is described, illustrated and compared with closely related taxa. New combinations are suggested for eight taxa (i.e. Athallia inconnexa (for Lecanora inconnexa Nyl.), Calogaya safavidiorum (for Caloplaca safavidiorum S. Y. Kondr., in Kondratyuk et al.), Coppinsiella orbicularis stat. et comb. nov. (for Caloplaca substerilis subsp. orbicularis M. Haji Moniri, Vondrák et Malíček), Coppinsiella substerilis (for Caloplaca substerilis Vondrák, Palice et van den Boom, in Vondrák et al.), Coppinsiella ulcerosa (for Caloplaca ulcerosa Coppins et P. James), Lazarenkoella persica (for Xanthoria polycarpoides var. persica J. Steiner); Lazarenkoella polycarpoides (for Xanthoria polycarpoides J. Steiner), and Seawardiella lobulata (for Lecanora lobulata Flörke)). [ABSTRACT FROM AUTHOR]

Abstract Coursetia caribaea is geographically and morphologically the most variable species in the genus Coursetia and in the tribe Robinieae (Leguminosae, Papilionoideae). Because of potentially undetected species, we assessed the phylogenetic relationships among the eight taxonomic varieties of C. caribaea. Sampling included nuclear ribosomal internal transcribed spacer sequences from 489 Robinieae accessions representing all varieties of C. caribaea and 38 of the 40 species of Coursetia, in addition to chloroplast trnD-trnT sequences from 186 accessions. Separate and combined phylogenetic analyses resolved a clade of conspecific accessions of the Bolivian C. caribaea var. astragalina as sister to the central Andean Coursetia grandiflora clade. Also distantly related to Coursetia caribaea var. caribaea accessions were those of the coastal Oaxacan C. caribaea var. pacifica, which formed the sister clade to accessions of the central Andean C. caribaea var. ochroleuca. The estimated mean ages of the stem clades for these three lineages, 11, 7.7, and 7.7 Ma, respectively, contrasted to the estimated mean ages of the corresponding crown clades of 0, 0, and 1.5 Ma. The contrasting stem and crown ages suggest that these taxa, appropriately ranked as species, Coursetia astragalina, Coursetia diversifolia, and Coursetia ochroleuca, each have persisted over evolutionary time frames as distinct geographically localized populations in seasonally dry tropical forests and woodlands. [ABSTRACT FROM AUTHOR]

Tribe Marrubieae (Lamiaceae: Lamioideae) comprises about 91 species classified in four genera distributed from Europe to West and Central Asia and North Africa. Here, we present a phylogenetic analysis of cpDNA (rpl32-trnL, rps16, trnL intron, trnL-trnF spacer) and nuclear ribosomal (ITS) sequence data of 68 accessions representing all genera and most sections of Marrubieae. Our taxon sampling covers is dense for the genera Ballota and Marrubium, including a total of 60 of 85 currently recognized taxa (species and subspecies). Parsimony and Bayesian analyses of individual nrITS and cpDNA markers, as well as the combined plastid dataset, produced largely congruent trees. Our results confirm the monophyly of tribe Marrubieae. All analyses retrieved four well supported clades in the tribe. The phylogenetic position of the genera Acanthoprasium and Moluccella is consistent with previous studies and both are recovered as monophyletic. The most important result of the present study is the splitting of the genus Ballota, in its traditional concept, into two well-supported clades matching well with the genera Ballota and Pseudodictamnus. Moreover, Marrubium, in its current circumscription, is paraphyletic, but will become monophyletic by transferring Ballota deserti to this genus. In conclusion, we propose the recognition of five genera in tribe Marrubieae: Acanthoprasium, Ballota, Moluccella, Marrubium and the resurrected segregate Pseudodictamnus. The required new combinations are proposed. [ABSTRACT FROM AUTHOR]

The health status of the native grapevine Vitis vinifera subsp. sylvestris (Gmeli) Hegi in natural areas in Europe has received little attention. A survey was carried out on wild grapevines in Tuscany (Italy), where isolates of the Grapevine rupestris stem pitting virus (GRSPaV), Grapevine leafroll-associated virus 1 and 3 (GLRaV-1 and GLRaV-3) and Grapevine virus A (GVA) were detected. The complete coat protein (CP) region of these isolates was sequenced to investigate the relationship of the viral variants from Tuscan wild grapevines with isolates from different geographical origins. According to the phylogenetic analyses, GLRaV-1 and GLRaV-3 isolates from Tuscan wild grapevines clustered with isolates from cultivated grapevines with nucleotide sequence identities ranging from 66% to 87% and from 72.5% to 99% respectively, without any correlation between the distribution and geographical origin. Conversely, GRSPaV and GVA isolates clustered together with other Italian isolates from V. vinifera with nucleotide sequence identities ranging from 71.14% to 96.12% and from 73.5% to 92%, respectively. Our analysis of the whole amino acid sequences revealed a high conservation level for the studied proteins explained by a selective pressure on this genomic region, probably due to functional constraints imposed on CP, such as specific interactions with cellular receptors in the insect vectors necessary for successful transmission. In addition, analyses of genetic recombination suggest no significant point mutations that might play a significant role in genetic diversification. The dN/dS ratio also estimated a low number of non-silent mutations, highlighting the purifying selective pressure. The widespread distribution of the Rugose wood complex (GRSPaV and GVA associated disease) in comparison with the Grapevine Leafroll associated viruses (GLRaV-1 and -3) could explain the major geographical correlation found for the viral variants detected in Tuscany. [ABSTRACT FROM AUTHOR]

Abstract: The about 1,000 species of tintinnid ciliates are identified and classified almost exclusively based on their lorica features, although the shortcomings of this structure are well‐known, e.g. causing uncertain species limitations and nonmonophyletic taxa. Hence, the present redescription of Tintinnopsis everta Kofoid and Campbell, 1929 considers not only the lorica characteristics, but focuses on cell and genetic features. The species is redescribed from the North Atlantic and adjacent sea areas, namely the east coast of the USA, using live observation, protargol‐stained material, scanning electron microscopy, and genetic analyses. The main stages of cell division are described, and the species’ phylogenetic relationships are inferred from morphological data and the small subunit ribosomal RNA gene sequence. The estimates of its biogeographical distribution and autecology are based on a literature survey. The species is characterised by a complex somatic ciliary pattern with a unique position of the posterior kinety and a conspicuously large distance between the somatic ciliary fields and the collar membranelles. The phylogenetic relationships of Tintinnopsis everta vary in the molecular trees depending on the algorithms used and are, therefore, regarded as unresolved. Nevertheless, the new kind of complex somatic ciliary pattern distinctly contributes to a better understanding of the tintinnid biodiversity and evolution and provides features for a future split of the nonmonophyletic genus Tintinnopsis. [ABSTRACT FROM AUTHOR]

In general, the chloroplast genomes of angiosperms are considered to be highly conserved and affected little by adaptive evolution. In this study, we tested this hypothesis based on sequence differentiation and adaptive variation in the plastid genomes in the order Dipsacales. We sequenced the plastid genomes of one Adoxaceae species and six Caprifoliaceae species, and together with seven previously released Dipsacales chloroplasts, we determined the sequence variations, evolutionary divergence of the plastid genomes, and phylogeny of Dipsacales species. The chloroplast genomes of Adoxaceae species ranged in size from 157,074 bp (Sinadoxa corydalifolia) to 158,305 bp (Sambucus williamsii), and the plastid genomes of Caprifoliaceae varied from 154,732 bp (Lonicera fragrantissima var. lancifolia) to 156,874 bp (Weigela florida). The differences in the number of genes in Caprifoliaceae and Adoxaceae species were largely due to the expansion and contraction of inverted repeat regions. In addition, we found that the number of dispersed repeats (Adoxaceae = 37; Caprifoliaceae = 384) was much higher than that of tandem repeats (Adoxaceae = 34; Caprifoliaceae = 291) in Dipsacales species. Interestingly, we determined 19 genes with positive selection sites, including three genes encoding ATP protein subunits (atpA, atpB, and atpI), four genes for ribosome protein small subunits (rps3, rps7, rps14, and rps15), four genes for photosystem protein subunits (psaA, psaJ, psbC, and pabK), two genes for ribosome protein large subunits (rpl22 and rpl32), and the clpP, infA, matK, rbcL, ycf1, and ycf2 genes. These gene regions may have played key roles in the adaptation of Dipsacales to diverse environments. In addition, phylogenetic analysis based on the plastid genomes strongly supported the division of 14 Dipsacales species into two previously recognized sections. The diversification of Adoxaceae and Caprifoliaceae was dated to the late Cretaceous and Tertiary periods. The availability of these chloroplast genomes provides useful genetic information for studying taxonomy, phylogeny, and species evolution in Dipsacales. [ABSTRACT FROM AUTHOR]

We report here the main characteristics of ‘Collinsella provencensis’ strain Marseille-P3740 (CSUR P3740), ‘Parabacteroides bouchesdurhonensis’ strain Marseille-P3763 (CSUR P3763) and ‘Sutterella seckii’ strain Marseille-P3660 (CSUR P3660), which were isolated using culturomics from the human gut microbiota of healthy individuals living in Marseille. [ABSTRACT FROM AUTHOR]

Phylodynamics of Crimean Congo Hemorrhagic fever virus (CCHFV) genotype V in South Russia was analyzed using 244 partial (452–571 nt) sequences in all three genomic segments and 38 complete genomic sequences. Despite increased number of sequences, the Russian lineage of the European genotype V (commonly termed GtVa) was distinct from GtV isolates from Turkey and the Balkan countries. No geographic pattern was observed in phylogenetic subgrouping of CCHFV within South Russia. Identical isolates could be found at distant locations spaced by hundreds of kilometers, while relatively divergent viruses circulated in the same region. Full genome analysis indicated that reassortment events within GtVa occurred every few decades (median half-life of a non-reassortant node 30–40 years) and involved M and S segments. Therefore, in South Russia CCHFV represents a highly dynamic population of frequently reassorting viruses. [ABSTRACT FROM AUTHOR]

Background Late embryogenesis abundant (LEA) proteins were initially discovered about 35 years ago as accumulating late in embryogenesis of cotton seeds. Although abundant in seeds and pollens, these proteins have been found to protect cells against desiccation, cold, high temperature, and high salinity. Objective Here, we present the first comprehensive survey of LEA proteins and their encoding genes in Gastrodia elata , a well-known medicinal orchid in China. Moreover, we researched on LEA family evolutionary relationships and functional characteristics. Methods The LEA gene family in G. elata (GeLEAs) was cloned based on RNA-Seq data. In addition, all of GeLEA genes were introduced into Escherichia coli to assess the function of GeLEAs under low temperature stress. Results Based on the phylogenetic analysis with Arabidopsis and Oryza LEA proteins, we identified 8 LEA protein encoding genes in G. elata that could be classified into 6 distinct subgroups. The motif composition of these proteins was an important feature specific to LEA groups. Compared with control, the expressions of 5 GeLEAs in E. coli exhibited enhanced cold resistance and viability, indicating that GeLEAs protein could play a protective role in cells under low temperature stress. Conclusion Our results suggest that LEAs from G. elata play an important role in responses to abiotic stress. [ABSTRACT FROM AUTHOR]

Fritillaria spp. constitute important traditional Chinese medicinal plants. Xinjiang is one of two diversity hotspots in China in which eight Fritillaria species occur, two of which are endemic to the region. Furthermore, the phylogenetic relationships of Xinjiang Fritillaria species (including F. yuminensis) within the genus are unclear. In the present study, we sequenced the chloroplast (cp) genomes of seven Fritillaria species in Xinjiang using the Illumina HiSeq platform, with the aim of assessing the global structural patterns of the seven cp genomes and identifying highly variable cp DNA sequences. These were compared to previously sequenced Fritillaria cp genomes. Phylogenetic analysis was then used to evaluate the relationships of the Xinjiang species and assess the evolution of an undivided stigma. The seven cp genomes ranged from 151,764 to 152,112 bp, presenting a traditional quadripartite structure. The gene order and gene content of the seven cp genomes were identical. A comparison of the 13 cp genomes indicated that the structure is highly conserved. Ten highly divergent regions were identified that could be valuable in phylogenetic and population genetic studies. The phylogenetic relationships of the 13 Fritillaria species inferred from the protein-coding genes, large single-copy, small single-copy, and inverted repeat regions were identical and highly resolved. The phylogenetic relationships of the species corresponded with their geographic distribution patterns, in that the north group (consisting of eight species from Xinjiang and Heilongjiang in North China) and the south group (including six species from South China) were basically divided at 40°N. Species with an undivided stigma were not monophyletic, suggesting that this trait might have evolved several times in the genus. [ABSTRACT FROM AUTHOR]

Subtribe Spiranthinae is the most species-rich lineage of terrestrial Neotropical orchids, encompassing > 500 species and 40 genera. We conducted maximum parsimony and maximum likelihood phylogenetic analyses of DNA sequence data of plastid matK-trnK and trnL-trnF and nuclear ribosomal ITS sequences for 36 genera and 182 species of Spiranthinae plus appropriate outgroups. The results strongly support monophyly of Spiranthinae (minus Discyphus, Discyphinae and Galeottiella, Galeottiellinae) and five major lineages, namely monospecific Cotylolabium (sister to the remaining Spiranthinae) and the Eurystyles, Pelexia, Spiranthes and Stenorrhynchos clades. Eighteen of the 27 genera of Spiranthinae for which more than one species was included in our analyses are monophyletic. Paraphyly of large genera, such as Cyclopogon and Sarcoglottis, resulted from segregation of particular species or groups of species exhibiting minor modifications of structures directly involved in pollination (e.g. nectary, rostellum and viscidium). Conversely, polyphyly has resulted from convergent evolution of floral attributes in distantly related species (e.g. Mesadenus). Some of the morphological characters used traditionally for generic delimitation and in nonmolecular cladistic analyses of Spiranthinae are discussed against the evolutionary framework set by our molecular trees, emphasizing putative synapomorphies and problems derived from inappropriate character coding or incorrect homology assessments. Our ancestral area analysis indicates that Spiranthinae originated in eastern South America, with subsequent migrations and secondary radiations in Mesoamerica and North America, plus a derived migration from the latter region to the Old World (Spiranthes). [ABSTRACT FROM AUTHOR]

Abstract: The genus Triptilion is endemic to central Chile, the Mendoza Province and western Patagonia in Argentina. It is currently composed of seven species: T. achilleae, T. benaventii, T. berteroi, T. capillatum, T. cordifolium, T. gibbosum, and T. spinosum. The main objectives of this paper were to determine the phylogenetic relationships of species of Triptilion. We also traced the evolution of annual and perennial life‐forms. Historically a close relationship has been described between genera Triptilion and Nassauvia. Phylogenetic analysis of the genus Triptilion and more closely related genera was undertaken using two nuclear (ITS, ETS) and two chloroplast (trnL‐F, rpl32‐trnL) markers. The topology of the Bayesian inference tree shows that the genus Triptilion is paraphyletic, because Nassauvia lagascae, the only representative of Nassauvia section Caloptilium grouped with T. achilleae, Clade I. The other species of Triptilion form two clades: Clade II composed of T. cordifolium and T. gibbosum and Clade III that includes T. benaventii, T. berteroi, T. capillatum, and T. spinosum. The genus Triptilion originated and diverged during the Miocene. The results of the life history reconstructions indicate that the common ancestor of Triptilion and Nassauvia was perennial. The annual habit appears to be derived in Triptilion. The life‐form of the common ancestor of Triptilion was ambiguous; it may have been annual or perennial. [ABSTRACT FROM AUTHOR]

A phylogenetic hypothesis for tribe Podochileae with emphasis on subtribe Eriinae s.s. is based on nucleotide sequences of the nuclear ITS and four plastid regions (matK, trnL-F spacer, trnL intron and ycf1). The strict consensus tree based on parsimony is largely congruent with the maximum likelihood tree with a few major differences; most importantly, monophyly of Podochileae as recently circumscribed is strongly supported by the maximum likelihood tree but not recovered in the parsimony analysis. Monophyly of Thelasiinae s.s. (without Ridleyella) and Eriinae s.l. (including Podochilinae) is supported, whereas Eria s.l. appears polyphyletic. The generic circumscription of Eriinae s.s. (excluding Podochilinae) is revised, and 21 genera are accepted, including two not previously recognized. Nomenclatural changes and a key to genera in Eriinae are provided. [ABSTRACT FROM AUTHOR]

The Nidularioid complex, as formed by the genera Nidularium Lem., Wittrockia Lindm., Neoregelia L.B.Sm., Canistropsis (Mez) Leme and Edmundoa Leme, is a Bromelioideae group known for its difficult generic delimitation. This difficulty is attributed to the large number of nonexclusive characters that are used in these genera, which demonstrates their intimate relationship. In current phylogenies, the genera belonging to the Nidularioid complex always emerge as a unified group termed as ‘Nidularioid Clade'. This study aims to reconstruct usual morphological characters in Bromelioideae, as well as anatomical characters from the leaf sheath and blade of species from the Nidularioid complex, in order to propose new synapomorphies for the group. To accomplish this, we proposed a phylogenetic hypothesis that used chloroplastidial atp B- rbc L, mat K, trn L- trn F and nuclear PhyC gene sequences obtained from the NCBI portal in a Bayesian analysis that resulted in a consensus tree. We also used parsimony and Bayesian methods to reconstruct previously delimited morphoanatomical characters. Our results indicate that the morphological characters typically used in the group's taxonomy represent homoplasies. Some anatomical characters are also homoplastic, such as the number of layers in the abaxial mechanical hypoderm from the leaf sheath. However, leaf anatomy provided new synapomorphies for the group, such as the presence of trichomes with elongated wing cells, the presence of adaxial epidermal cells with slightly thickened walls on the leaf blade and brachiform cells with long branches in the leaf sheath region. Thus, this paper presents new perspectives for future studies on the evolution of characters in the Nidularioid complex. [ABSTRACT FROM AUTHOR]

The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity. [ABSTRACT FROM AUTHOR]

Echinocereusis a morphologically diverse genus that includes 64 species grouped into eight taxonomic sections based on morphological traits. In previous molecular phylogenetic analyses, the relationships amongstEchinocereusspecies were not entirely revealed and useful characters to recognize clades were not provided. The inclusion of several sources of evidence in a phylogenetic analysis is likely to produce more supported hypotheses. Therefore, we performed a combined phylogenetic analysis with a set of 44 morphological characters and six chloroplast DNA sequences. Topologies from parsimony and Bayesian analyses were mostly congruent. However, the relationships ofE. poselgeriwere not consistent between analyses. A second Bayesian analysis using a long-branch extraction test resulted in a topology with the morphological position ofE. poselgericongruent with that in parsimony analysis. Parsimony and Bayesian analyses corroborated the monophyly ofEchinocereus, which included eight monophyletic groups. The combined phylogeny integrated into different clades those taxa that were not determined in previous analyses and changed the relationships of some recognized clades. The clades did not recover the recent infrageneric classification. In the present study, a new sectional classification forEchinocereusis proposed based on the eight recovered clades, which is supported by a combination of morphological and molecular characters. An identification key for sections in the genus is included. [ABSTRACT FROM AUTHOR]

Subtribe Gonolobinae of the cosmopolitan family Apocynaceae is diverse and represents the largest radiation of milkweeds in the New World (~500 species). The largest genus, Matelea, is an amalgam that was united largely by a perceived lack of discrete morphological variation, particularly in floral structures. Using plastid and nuclear DNA sequences, we estimate a phylogeny of Gonolobinae using four chloroplast loci and three cloned nuclear regions. We investigate the monophyly of Matelea and other established and provisional genera via a series of hypothesis tests. We find variable support and considerable conflict among the gene trees. Despite this, our data confirm the paraphyly of Matelea, while Gonolobus and other segregate genera receive some support as monophyletic assemblages. We attribute conflicting signal in our data primarily to incomplete lineage sorting, a likely result of rapid radiation. Ancestral character reconstructions of growth foim, fruit, and corolla morphology reveal a woody twining growth form to be plesiomorphic with one to two transitions to an herbaceous, non-twiriing growth form followed by one putative reversal to the woody twining growth form in the subtribe. Plesiomorphic states for fruit ornamentation and corolla shape are less clear, and these characters exhibit high levels of homoplasy. This study is one of the most comprehensive phylogeriies of gonoloboid milkweeds to date and the first to sample multiple nuclear loci and include allelic data. [ABSTRACT FROM AUTHOR]

Objective: Borassus flabellifer or Asian Palmyra palm is widely distributed in South and Southeast Asia and is horticultural and economic importance for its fruit and palm sugar production. However, its population is in rapid decline, and only a few genetic data are available. We sequenced the complete chloroplast (cp) genome of B. flabellifer to provide its genetic data for further utilization. Results: The cp genome was obtained by Illumina sequencing and manual gap fillings providing 160,021 bp in length containing a pair of inverted repeats (IRs) with 27,256 bp. These IRs divide the genome into a large single copy region 87,444 bp and a small single copy region 18,065 bp. In total, 113 unique genes, 134 SSRs and 47 large repeats were identified. This is the first complete cp genome reported in the genus Borassus. A comparative analysis among members of the Borasseae tribe revealed that the B. flabellifer cp genome is, so far, the largest and the cp genomes of this tribe have a similar structure, gene number and gene arrangement. A phylogenetic tree reconstructed based on 74 protein-coding genes from 70 monocots demonstrates short branch lengths indicating slow evolutionary rates of cp genomes in family Arecaceae. [ABSTRACT FROM AUTHOR]

Background: Elytrigia Desv. is a genus with a varied array of morphology, cytology, ecology, and distribution in Triticeae. Classification and systematic position of Elytrigia remain controversial. We used nuclear internal-transcribed spacer (nrITS) sequences and chloroplast trnL-F region to study the relationships of phylogenetic and maternal genome donor of Elytrigia Desv. sensu lato. Results: (1) E, F, P, St, and W genomes bear close relationship with one another and are distant from H and Ns genomes. Ee and Eb are homoeologous. (2) In ESt genome species, E genome is the origin of diploid Elytrigia species with E genome, St genome is the origin of Pseudoroegneria. (3) Diploid species Et. elongata were differentiated. (4) Et. stipifolia and Et. varnensis sequences are diverse based on nrITS data. (5) Et. lolioides contains St and H genomes and belongs to Elymus s. l. (6) E genome diploid species in Elytrigia serve as maternal donors of E genome for Et. nodosa (PI547344), Et. farcta, Et. pontica, Et. pycnantha, Et. scirpea, and Et. scythica. At least two species act as maternal donor of allopolyploids (ESt and EStP genomes). Conclusions: Our results suggested that Elytrigia s. l. species contain different genomes, which should be divided into different genera. However, the genomes of Elytrigia species had close relationships with one another. Diploid species were differentiated, because of introgression and different geographical sources. The results also suggested that the same species and the same genomes of different species have different maternal donor. Further study of molecular biology and cytology could facilitate the evaluation of our results of phylogenetic in a more specific and accurate way. [ABSTRACT FROM AUTHOR]

Background and Aims The 'orchid-like' bladderworts (Utricularia) comprise 15 species separated into two sections: Orchidioides and Iperua. These robust and mostly epiphytic species were originally grouped within the section Orchidioides by the first taxonomical systems. These species were later split into two sections when sect. Iperua was proposed. Due to the lack of strong evidence based on a robust phylogenetic perspective, this study presents a phylogenetic proposal based on four different DNA sequences (plastid and nuclear) and morphology to test the monophyly of the two sections. Methods In comparison with all previous phylogenetic studies, the largest number of species across the sections was covered: 11 species from sections Orchidioides and Iperua with 14 species as an external group. Maximum likelihood and Bayesian inferences were applied to DNA sequences of rps16, trnL-F, matK, the internal transcribed spacer (ITS) and three morphological characters: (1) the crest of the corolla; (2) the primary organs in the embryo; and (3) tubers. Additionally, a histochemical analysis of the stolons and tubers is presented from an evolutionary perspective. Key Results The analyses showed the paraphyly of sect. Iperua, since Utricularia humboldtii is more related to the clade of sect. Orchidioides. Utricularia cornigera is grouped in the sect. Iperua clade based on chloroplast DNA sequences, but it is nested to sect. Orchidioides according to ITS dataset. Morphological characters do not support the breaking up of the 'orchid-like' species into two sections, either. Moreover, the stolon-tuber systems of both sections serve exclusively for water storage, according to histological analyses. Conclusions This study provides strong evidence, based on DNA sequences from two genomic compartments (plastid and nucleus) and morphology to group the Utricularia sect. Orchidioides into the sect. Iperua. The tubers are important adaptations for water storage and have been derived from stolons at least twice in the phylogenetic history of 'orchid-like' bladderworts. [ABSTRACT FROM AUTHOR]

Members of the sea anemone genus Anthopleura are familiar constituents of rocky intertidal communities. Despite its familiarity and the number of studies that use its members to understand ecological or biological phenomena, the diversity and phylogeny of this group are poorly understood. Many of the taxonomic and phylogenetic problems stem from problems with the documentation and interpretation of acrorhagi and verrucae, the two features that are used to recognize members of Anthopleura. These anatomical features have a broad distribution within the superfamily Actinioidea, and their occurrence and exclusivity are not clear. We use DNA sequences from the nucleus and mitochondrion and cladistic analysis of verrucae and acrorhagi to test the monophyly of Anthopleura and to evaluate the pattern of distribution of acrorhagi and verrucae. We find that Anthopleura is paraphyletic: although species of the genus cluster together, some groups also include members of genera like Bunodosoma, Aulactinia, Oulactis, and Actinia. This paraphyly is explained in part by the discovery that acrorhagi and verrucae are pleisiomorphic for the subset of Actinioidea studied. [ABSTRACT FROM AUTHOR]

Parasenecio with c. 70 species is a major component of the eastern Asian Tussilagininae (Asteraceae, Senecioneae). Previous molecular phylogenetic studies, although with limited taxon sampling, have suggested that it is polyphyletic and forms a complex with ten other eastern Asian genera of Tussilagininae, i.e. the Ligularia-Cremanthodium- Parasenecio (LCP) complex. Here we sample Parasenecio and its relatives in the LCP complex densely and generate two phylogenetic hypotheses for the genus using four plastid DNA (trnCGCA-petN, trnGUCC-trnTGGU-psbD, trnTUGUtrnLUAA and rpl32-ndhF) and two nuclear ribosomal (nr)DNA [internal and external transcribed spacer (ITS and ETS)] regions, respectively. Analyses of the plastid DNA data produce a robust generic-level phylogenetic tree for Parasenecio and clearly demonstrate the polyphyletic pattern of the genus. Most notably, two sections of Parasenecio, P. section Delphiniifolii s.s. and P. section Taimingasa, are shown to be distantly related to core Parasenecio, being sister to Miricacalia and Syneilesis, respectively, with strong support. The small genus Sinacalia is also revealed to be polyphyletic, with S. caroli nested in core Parasenecio, and S. tangutica and S. davidii forming a clade sister to the core Parasenecio-S. caroli clade. The nrDNA tree is, however, relatively poorly resolved, only confirming the sister relationship between P. section Delphiniifolii s.s. and Miricacalia. Sinacalia s.s. is resolved as being deeply nested in core Parasenecio with nrDNA data, which is the only significant incongruence with the plastid DNA hypothesis relevant to the generic circumscription of Parasenecio. Statistical topology (approximately unbiased and Swofford- Olsen-Waddell-Hillis) tests suggest that, except for the position of Sinacalia s.s., the generic-level relationships of Parasenecio inferred from the plastid DNA data are not incongruent with those from the nrDNA data and, on the basis of current sequence data, the inferred molecular phylogenetic relationships should be preferred over the current classification. Based on these results and evidence from morphology and karyology, we propose a new circumscription of Parasenecio, involving transferring S. caroli to Parasenecio as P. caroli comb. nov. and segregating P. section Delphiniifolii s.s. and P. section Taimingasa as the new genera Japonicalia gen. nov. and Taimingasa gen. nov., respectively. Sinacalia s.s., with significant incongruence between the plastid DNA and nrDNA trees, is tentatively retained as an independent genus pending future studies. A revised key to Parasenecio and its close relatives is provided. [ABSTRACT FROM AUTHOR]

Four new orchid species and one variety from the cerrado and campos rupestres of central and south-eastern Brazil are described and illustrated: Habenaria brachydactyla, H. irwiniana, H. minuta, H. pansarinii, and H. pansarinii var. minuscula. Habenaria campylogyna is proposed as a new name for the illegitimate H. humilis Cogniaux. The five species differ from other Neotropical taxa by being small, slender plants with linear leaves concentrated at the base of the stem. Molecular phylogenetic analyses based on nuclear and plastid DNA sequences revealed that they are not closely related, and do not belong to any of the previously identified Neotropical subclades. All of the new taxa were recovered in isolated positions, branching from basal nodes of larger subclades, suggesting that these morphological characters represent plesiomorphic traits in the Neotropical clade. Habenaria brachydactyla is genetically distinct and represents an early lineage of the Neotropical Habenaria clade. All taxa are considered threatened because of their small numbers of populations with few individuals and/or restricted distributions. Detailed descriptions, photographs, illustrations, notes, and a key to the species are presented. [ABSTRACT FROM AUTHOR]

This study presents the first molecularly proven data on natural hybridization in the genus Pulsatilla, including the complete plastome sequence. A plant with morphological characteristics intermediate between P. patens and P. pratensis was found near the village of Bocheniec (southern Poland). In this study, several classes of markers based on genotyping (SSR and ISJ) and sequencing (Sanger and NGS) were used to confirm hybridization and its direction, and to determine the prospective parent species. Analysis of ISJ and ISSR genotyping data revealed that all amplified loci were polymorphic. The hybrid species was characterized by only 3 specific bands, and it shared the highest number of bands with P. pratensis. A total of 3,204,448 pair-end reads (2 x 250 bp) from Pulsatilla x hackelii were obtained in a single run of the MiSeq sequencer. The structure of the hybrid plastid genome did not differ from the previously identified genomes of the Pulsatilla species. A phylogenetic analysis of plastomes in the Pulsatilla species revealed three well-supported clades. The plastome of Pulsatilla x hackelii was included in the P. pratensis clade. P. hackelii and P. pratensis formed a well-supported clade, and their plastomes differed by 78 substitutions and 74 indels. Most of these differences were found in intergenic noncoding regions (52 substitutions and 67 indels) and introns (11 substitutions and 5 indels). The sequenced plastid genome of the hybrid species was most similar to Pulsatilla pratensis, which suggests that the analyzed P. pratensis specimen was pollinated by P. patens. [ABSTRACT FROM AUTHOR]

Gaultheria trichophylla var. tetracme of G. series Trichophyllae (Ericaceae) has been distinguished from the nominate variety of G. trichophylla by the presence of two awns on each anther theca (versus one). Phylogenetic data based on plastid DNA sequences placed G. t. var. tetracme in a different clade than the nominate variety with strong statistical support, suggesting that G. trichophylla is not monophyletic. To investigate this further, we studied the morphology of these two taxa in the field and with herbarium material. We found that G. t. var. tetracme differs substantially from the nominate variety in morphology, not only by the number of anther awns, but also the larger size of many features, e.g., plant height, leaves, and pedicels, a greater number of leaf marginal setae, and a distinct geographic range. On this basis, we elevate G. t. var. tetracme to the species level as Gaultheria tetracme, endemic to the Hengduan Shan in Sichuan Province, China. We note the wide morphological variation in the remainder of G. trichophylla and indicate specific problems that should be investigated in more detail for better understanding the taxonomy of this species. [ABSTRACT FROM AUTHOR]

Hybridization is a frequent and important force in plant evolution. Next-generation sequencing (NGS) methods offer new possibilities for clade resolution and ambitious sampling of gene genealogies, yet difficulty remains in detecting deep reticulation events using currently available methods. We reconstructed the phylogeny of diploid representatives of Amaryllidaceae tribe Hippeastreae to test the hypothesis of ancient hybridizations preceding the radiation of its major subclade, Hippeastrinae. Through hybrid enrichment of DNA libraries and NGS, we obtained data for 18 nuclear loci through a curated assembly approach and nearly complete plastid genomes for 35 ingroup taxa plus 5 outgroups. Additionally, we obtained alignments for 39 loci through an automated assembly algorithm. These data were analyzed with diverse phylogenetic methods, including concatenation, coalescence-based species tree estimation, Bayesian concordance analysis, and network reconstructions, to provide insights into the evolutionary relationships of Hippeastreae. Causes for gene tree heterogeneity and cytonuclear discordance were examined through a Bayesian posterior predictive approach (JML) and coalescent simulations. Two major clades were found, Hippeastrinae and Traubiinae, as previously reported. Our results suggest the presence of two major nuclear lineages in Hippeastrinae characterized by different chromosome numbers: (1) Tocantinia and Hippeastrum with 2n = 22, and (2) Eithea , Habranthus , Rhodophiala , and Zephyranthes mostly with 2n = 12, 14, and 18. Strong cytonuclear discordance was confirmed in Hippeastrinae, and a network scenario with at least six hybridization events is proposed to reconcile nuclear and plastid signals, along a backbone that may also have been affected by incomplete lineage sorting at the base of each major subclade. [ABSTRACT FROM AUTHOR]

Based on a worldwide phylogenetic framework filling the taxonomic gap of Madagascar and surrounding islands of the Western Indian Ocean (WIO), we revisited the systematics of grammitid fern species (Polypodiaceae). We also investigated the biogeographic origin of the extant diversity in Madagascar and estimated the relative influence of vicariance, long-distance dispersals (LDD) and in situ diversification. Phylogenetic inferences were based on five plastid DNA regions ( atpB , rbcL , rps4-trnS , trnG-trnR , trnL-trnF ) and the most comprehensive taxonomic sampling ever assembled (224 species belonging to 31 out of 33 recognized grammitids genera). 31 species from Madagascar were included representing 87% of the described diversity and 77% of the endemics. Our results confirmed a Paleotropical clade nested within an amphi-Atlantic grade. In addition, we identified three new major clades involving species currently belonging to Grammitis s.l. , Ctenopterella and Enterosora . We resolved for the first time Grammitis s.s. as monophyletic, and Ctenopterella (newly tested here) and Enterosora as polyphyletic. The Neotropical genus Moranopteris was shown to also occur in Madagascar through a newly discovered species. Most importantly, we suggest a >30% inflation of the species number in the WIO due to the hidden diversity in >10 cryptic lineages, best explained by high morphological homoplasy. Molecular dating and ancestral areas reconstruction allowed identifying the Neotropics as the predominant source of LDD to the African-WIO region, with at least 12 colonization events within the last 20 Ma. Repeated eastward migrations may be explained by transoceanic westerly winds transporting the dust-like spores. Tropical Asia s.l. would also have played a (minor) role through one dispersal event to Madagascar at the end of the Oligocene. Last, within the complex Malagasy region made of a mosaic of continental and oceanic islands located close to the African continent, we showed that contrary to theoretical expectations and empirical evidence in angiosperms, Africa does not act as a dispersal source and Madagascar seems to have a more important influence on the regional dynamics: we observed both in situ species diversification and dispersal out of Madagascar. This influence also extends beyond the region, since one dispersal event probably originated from Madagascar and reached the Subantarctic island of Amsterdam. [ABSTRACT FROM AUTHOR]

Cotton ( Gossypium spp.) is commonly grouped into eight diploid genomic groups, designated A-G and K, and an allotetraploid genomic group, AD. Gossypium raimondii (D5) and G. arboreum (A2) are the putative contributors to the progenitor of G. hirsutum ( AD1), the economically important fibre-producing cotton species., Mitochondrial DNA from week-old etiolated seedlings was extracted from isolated organelles using discontinuous sucrose density gradient method. Mitochondrial genomes were sequenced, assembled, annotated and analysed in orderly., Gossypium raimondii (D5) and G. arboreum (A2) mitochondrial genomes were provided in this study. The mitochondrial genomes of two diploid species harboured circular genome of 643,914 bp (D5) and 687,482 bp (A2), respectively. They differ in size and number of repeat sequences, both contain illuminating triplicate sequences with 7317 and 10,246 bp, respectively, demonstrating dynamic difference and rearranged genome organisations. Comparing the D5 and A2 mitogenomes with mitogenomes of tetraploid Gossypium species ( AD1, G. hirsutum; AD2, G. barbadense), a shared 11 kbp fragment loss was detected in allotetraploid species, three regions shared by G. arboreum (A2), G. hirsutum ( AD1) and G. barbadense ( AD2), while eight regions were specific to G. raimondii (D5). The presence/absence variations and gene-based phylogeny supported that A-genome is a cytoplasmic donor to the progenitor of allotetraploid species G. hirsutum and G. barbadense., The results present structure variations and phylogeny of Gossypium mitochondrial genome evolution. [ABSTRACT FROM AUTHOR]

In this study, we surveyed the bacteriome-associated microbiota of the corn leafhopper Dalbulus maidis by means of histological, ultrastructural, and molecular analyses. Amplification and sequencing of 16S rDNA genes revealed that the endosymbiont ' Candidatus Sulcia muelleri' (Phylum Bacteroidetes) resides in bacteriomes of D. maidis. Phylogenetic analysis showed that the sequence was closely allied to others found in representatives of the subfamily Deltocephalinae. We failed to amplify other sequences as ' Candidatus Nasuia deltocephalinicola,' a co-primary symbiont frequently associated to deltocephaline leafhoppers. In addition, a metagenetic analysis carried out in order to investigate the presence of other bacteriome-associated bacteria of D. maidis showed that the sequence of Sulcia accounted for 98.56 % of all the sequences. Histological and ultrastructural observations showed that microorganisms harbored in bacteriomes (central syncytium and cytoplasm of uninucleate bacteriocytes) look like others Sulcia described in hemipteran species and they were transovarially transmitted from mother to offspring which is typical of obligate endosymbionts. The only presence of Sulcia in the bacteriomes of D. maidis was discussed. [ABSTRACT FROM AUTHOR]

Abstract: Restriction site‐associated DNA sequencing (RAD‐seq) was used to illuminate the genetic relationships among Eriobotrya species. The raw data were filtered, and 221 million clean reads were used for further analysis. A total of 1,983,332 SNPs were obtained from 23 Eriobotrya species and two relative genera. We obtained similar results by neighbor‐joining and maximum likelihood phylogenetic trees. All Eriobotrya plants grouped together into a big clade, and two out‐groups clustered together into a single or separate clade. Chinese and Vietnam accessions were distributed throughout the dendrogram. There was nonsignificant correlation between genotype and geographical distance. However, clustering results were correlated with leaf size to some extent. The Eriobotrya species could be divided into following three groups based on leaf size and phylogenetic analysis: group A and group B comprised of small leaves with <10 cm length except E. stipularis (16.76 cm), and group C can be further divided into two subgroups, which contained medium‐size leaves with a leaf length ranged from 10 to 20 cm and a leaf length bigger than 20 cm. [ABSTRACT FROM AUTHOR]

WRKY proteins are a large family of plant transcription factors, which play an important role in many biological processes such as plant development, metabolism, and responses to biotic and abiotic stresses. This study aimed to develop a complete overview of the WRKY family by using the potato genome. Based on the genome-wide analysis, a total of 82 StWRKY proteins were characterized and classified into three groups (I, II, and III) and five subgroups (IIa, IIb, IIc, IId, and IIe) according to the sequence similarity, motif varieties, and their phylogenetic relationships. By using multiple sequence alignment, a novel motif, WRKYGQR, was identified from StWRKY076 along with three variations of the WRKYGQK heptapeptide (WRKYGMK, WHKCGQK, and WRKYGKK) that might execute new biological functions. Chromosomal location analysis showed that the 82 StWRKY proteins were located in 11 of the 12 chromosomes, excluding chromosome 11. Phylogenetic analyses also showed that the 82 StWRKY proteins could be clustered into three large groups and five subgroups which shared typical characters of WRKY. The results provide fundamental information to inform further analysis and understanding of WRKY gene functions in potato. [ABSTRACT FROM AUTHOR]

The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants the molecular signals of genome duplications have remained largely unexplored. High-throughput transcriptome data from next-generation sequencing have set the stage for novel investigations of genome evolution using new bioinformatic and methodological tools in a phylogenetic framework. Here we compare ten de novo-assembled transcriptomes representing the major lineages of the angiosperm genus Cornus (dogwood) and relevant outgroups using a customized pipeline for analyses. Using three distinct approaches, molecular dating of orthologous genes, analyses of the distribution of synonymous substitutions between paralogous genes, and examination of substitution rates through time, we detected a shared WGD event in the late Cretaceous across all taxa sampled. The inferred doubling event coincides temporally with the paleoclimatic changes associated with the initial divergence of the genus into three major lineages. Analyses also showed an acceleration of rates of molecular evolution after WGD. The highest rates of molecular evolution were observed in the transcriptome of the herbaceous lineage, C. canadensis, a species commonly found at higher latitudes, including the Arctic. Our study demonstrates the value of transcriptome data for understanding genome evolution in closely related species. The results suggest dramatic increase in sea surface temperature in the late Cretaceous may have contributed to the evolution and diversification of flowering plants. [ABSTRACT FROM AUTHOR]

LEAFY COTYLEDON1 (LEC1) is a HAP3 subunit of CCAAT-binding transcription factor. The species in the genus Isoetes L. from China include I. hypsophila, I. yunguiensis, I. sinensis, I. orientalis, and I. taiwenensis. In this study, we initially gathered substantial samples from wide geographic ranges in China. Then we explored the evolutionary characteristics and expression profiles of LEC1 in Isoetes from China. We amplified 57 unique LEC1 nucleotide sequences from 94 individuals. The value of nucleotide diversity was 0.01693 for all samples, and neutrality tests indicated that LEC1 is under purifying negative selection in the evolutionary process. AMOVA analysis revealed that the genetic variation occurred mainly among populations within species. Moreover, the non-synonymous to synonymous substitution rates for 41 unique LEC1 protein sequences further demonstrated the presence of negative selection acting on the species from China to fix amino acid residues. Phylogenetic analyses of nucleotide and protein sequences showed consistently that the trees consisted of two well-supported main clades, and that the haplotypes from H42 to H57 in I. hypsophila were exclusive. In addition, expression profile analysis revealed that LEC1 transcripts accumulated primarily in reproductive organs. Looking at drought tolerance, LEC1 transcripts increased markedly at 24 h after drought treatment and reached a peak at 48 h. RNA accumulation reoccurred at relatively low levels and was slightly elevated at 48 h after rehydration. Altogether, our analyses provide insight into the evolutionary process of LEC1, and our results might promote further studies of functional genes in Isoetes. [ABSTRACT FROM AUTHOR]

Erysimum damirliense, a new species of Brassicaceae from Zanjan and Ardebil provinces (northwest Iran) is described and illustrated. The new species resembles E. uncinatifolium and E. elbrusense, but is easily recognized by its life form, basal leaf margin, indumentum of cauline leaves, number of flowers in the main raceme, fruit width and style length. Phylogenetic analysis of internal transcribed spacer (ITS) DNA sequences confirm that the new species is distinct from morphologically similar species. [ABSTRACT FROM AUTHOR]

The phylogenetic relationships of 31 genera of the traditional grass tribe Aveneae, with focus on Southeast Asian species of Helictotrichon, were examined using DNA sequences of the plastid matK-psbA region, nuclear ITS, the nuclear single-copy gene topoisomerase 6 (Topo6) spanning two introns and morphology. A molecular phylogenetic analysis was performed for 121 species applying maximum parsimony and Bayesian methods. Additionally we surveyed 11 Southeast Asian taxa for structural spikelet characters including lemmas, lodicules and ovaries. The phylogenetic results of the three molecular markers revealed that several Southeast Asian species traditionally accommodated in Helictotrichon are misplaced in this genus except for H. abietetorum, H. hideoi and H. leianthum. The placement of H. polyneurum and H. sumatrense in the genus Helictotrichon requires further investigation as suggested by morphological and preliminary molecular data. Due to the occurrence of different sequence types of ITS and Topo6, both nuclear DNA markers suggested an allopolyploid origin for several Southeast Asian taxa. (1) In Helictotrichon parviflorum and H. potaninii two different sequence types of Topo6 occur, closely similar to those of Trisetum and Helictotrichon, respectively. Nuclear ITS data of both species point to affinities with Trisetum and related genera but not to Helictotrichon. Both species belong to a hitherto unknown genus that is morphologically distinct from Trisetum and Helictotrichon and is named Tzveleviochloa. (2) Two copy types (A and B) of Topo6 previously identified in African Trisetopsis, a genus encompassing predominantly sub-Saharan species that traditionally had been ascribed to Helictotrichon, also occur in two Southeast Asian species, i.e., H. junghuhnii and H. virescens. In agreement with morpho- logical data both species need to be transferred to Trisetopsis. This expands the hitherto known eastern edge of the range of Trisetopsis from the Arabian Peninsula to China. (3) Additionally, the Chinese H. altius has a copy type sequence of Topo6 similar to that of Trisetopsis but not of Helictotrichon in its genome, whereas its plastid DNA fits Helictotrichon and relatives. Along with morphological characters this supports intermediacy between Trisetopsis and Helictotrichon. Therefore H. altius is probably an intergeneric hybrid, here named xTrisetopsotrichon altius. The taxonomically difficult genus Helictotrichon s.l. in tropical to temperate southeastern Asia becomes disassembled into Helictotrichon s.str., the new genus Tzveleviochloa, gen. nov., and the nothogenus xTrisetopsotrichon, nothogen. nov. The following combinations are introduced: Trisetopsis aspera, comb. nov., T. junghuhnii, comb. nov., T. virescens, comb. nov., xTrisetopsotrichon altius, comb. nov., Tzveleviochloa burmanica, comb. nov., T. parviflora, comb. nov., T. potaninii, comb. nov. [ABSTRACT FROM AUTHOR]

Background: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now. Description: We present the Nicotiana attenuata Data Hub (NaDH) as a centralized platform for integrating and visualizing genomic, phylogenomic, transcriptomic and metabolomic data in N. attenuata. The NaDH currently hosts collections of predicted protein coding sequences of 11 plant species, including two recently sequenced Nicotiana species, and their functional annotations, 222 microarray datasets from 10 different experiments, a transcriptomic atlas based on 20 RNA-seq expression profiles and a metabolomic atlas based on 895 metabolite spectra analyzed by mass spectrometry. We implemented several visualization tools, including a modified version of the Electronic Fluorescent Pictograph (eFP) browser, co-expression networks and the Interactive Tree Of Life (iTOL) for studying gene expression divergence among duplicated homologous. In addition, the NaDH allows researchers to query phylogenetic trees of 16,305 gene families and provides tools for analyzing their evolutionary history. Furthermore, we also implemented tools to identify co-expressed genes and metabolites, which can be used for predicting the functions of genes. Using the transcription factor NaMYB8 as an example, we illustrate that the tools and data in NaDH can facilitate identification of candidate genes involved in the biosynthesis of specialized metabolites. Conclusion: The NaDH provides interactive visualization and data analysis tools that integrate the expression and evolutionary history of genes in Nicotiana, which can facilitate rapid gene discovery and comparative genomic analysis. Because N. attenuata shares many genome-wide features with other Nicotiana species including cultivated tobacco, and hence NaDH can be a resource for exploring the function and evolution of genes in Nicotiana species in general. The NaDH can be accessed at: http://nadh.ice.mpg.de/. [ABSTRACT FROM AUTHOR]